Thanks. It was actually a related problem. The path of APBS had no spaces, but I though that "Working directory" was the path of VMD, which has spaces. I just changed "working directory" to a no spaces path and that solved the problem.
Hi Cuauhtemoc –
In order to run APBS under Windows, you need to invoke it through the command line or through VMD. Clicking on the icon does not work.
The most common reason for missing files in VMD is spaces in the path name for APBS and/or the APBS input files. Have you confirmed that your paths do not have spaces?
Pacific Northwest National Laboratory